scholarly journals Evolutionary Role of Restriction/Modification Systems as Revealed by Comparative Genome Analysis

2001 ◽  
Vol 11 (6) ◽  
pp. 946-958
Author(s):  
Eduardo P.C. Rocha ◽  
Antoine Danchin ◽  
Alain Viari
Keyword(s):  
Restriction Site ◽  
Bacterial Species ◽  
Genetic Material ◽  
Type Ii ◽  
Parasite Relationship ◽  
Host Parasite ◽  
Restriction Modification ◽  
Evolutionary Role ◽  
Restriction Modification Systems ◽  
Site Avoidance

Type II restriction modification systems (RMSs) have been regarded either as defense tools or as molecular parasites of bacteria. We extensively analyzed their evolutionary role from the study of their impact in the complete genomes of 26 bacteria and 35 phages in terms of palindrome avoidance. This analysis reveals that palindrome avoidance is not universally spread among bacterial species and that it does not correlate with taxonomic proximity. Palindrome avoidance is also not universal among bacteriophage, even when their hosts code for RMSs, and depends strongly on the genetic material of the phage. Interestingly, palindrome avoidance is intimately correlated with the infective behavior of the phage. We observe that the degree of palindrome and restriction site avoidance is significantly and consistently less important in phages than in their bacterial hosts. This result brings to the fore a larger selective load for palindrome and restriction site avoidance on the bacterial hosts than on their infecting phages. It is then consistent with a view where type II RMSs are considered as parasites possibly at the verge of mutualism. As a consequence, RMSs constitute a nontrivial third player in the host–parasite relationship between bacteria and phages.

scholarly journals Effects of mutations in phage restriction sites during escape from restriction–modification

2017 ◽  
Vol 13 (12) ◽  
pp. 20170646 ◽  
Author(s):  
Maroš Pleška ◽  
Călin C. Guet
Keyword(s):  
Restriction Site ◽  
Response To Selection ◽  
Modification System ◽  
Restriction Modification System ◽  
Restriction Sites ◽  
Restriction Modification ◽  
Insight Into ◽  
Restriction Modification Systems ◽  
Site Avoidance

Restriction–modification systems are widespread genetic elements that protect bacteria from bacteriophage infections by recognizing and cleaving heterologous DNA at short, well-defined sequences called restriction sites. Bioinformatic evidence shows that restriction sites are significantly underrepresented in bacteriophage genomes, presumably because bacteriophages with fewer restriction sites are more likely to escape cleavage by restriction–modification systems. However, how mutations in restriction sites affect the likelihood of bacteriophage escape is unknown. Using the bacteriophage λ and the restriction–modification system EcoRI, we show that while mutation effects at different restriction sites are unequal, they are independent. As a result, the probability of bacteriophage escape increases with each mutated restriction site. Our results experimentally support the role of restriction site avoidance as a response to selection imposed by restriction–modification systems and offer an insight into the events underlying the process of bacteriophage escape.

Comparative genomics of the Pasteurella multocida toxin

Genome ◽  
2021 ◽  
Author(s):  
Shivakumara Siddaramappa
Keyword(s):  
Pasteurella Multocida ◽  
Capsular Polysaccharide ◽  
Bacterial Species ◽  
Atrophic Rhinitis ◽  
Type Ii ◽  
Nucleotide Polymorphisms ◽  
Modification System ◽  
Restriction Modification System ◽  
Heat Labile ◽  
Restriction Modification

Pasteurella multocida is a zoonotic pathogen whose genetic heterogeneity is well known. Five serogroups and 16 serotypes of P. multocida have been recognized thus far based on capsular polysaccharide typing and lipopolysaccharide typing, respectively. Progressive atrophic rhinitis in domestic pigs is caused by P. multocida strains containing toxA, which encodes a heat-labile toxin. In this study, by comparative analyses of the genomes of many strains, it has been shown that toxA is sparsely distributed in P. multocida. Furthermore, full-length homologs of P. multocida toxA were found only in two other bacterial species. It has also been shown that toxA is usually associated with a prophage. Among the toxA-containing prophages that were compared, an operon putatively encoding a type II restriction-modification system was present only in strains LFB3, HN01, and HN06. These results indicate that the selection and maintenance of the heat-labile toxin and the type II restriction-modification system are evolutionarily less favorable among P. multocida strains. Phylogenetic analysis using the alignment- and parameter-free method CVTree3 showed that deduced proteome sequences can be used as effectively as whole/core genome single nucleotide polymorphisms to group P. multocida strains in relation to their serotypes and/or genotypes.

scholarly journals Regulation of genetic flux between bacteria by restriction–modification systems

2016 ◽  
Vol 113 (20) ◽  
pp. 5658-5663 ◽  
Author(s):  
Pedro H. Oliveira ◽  
Marie Touchon ◽  
Eduardo P. C. Rocha
Keyword(s):  
Gene Transfer ◽  
Bacterial Species ◽  
Innate Immune ◽  
Type Ii ◽  
Genetic Transfer ◽  
Double Stranded Dna ◽  
Restriction Sites ◽  
Similar Restriction ◽  
Dna Ends ◽  
Restriction Modification

Restriction–modification (R-M) systems are often regarded as bacteria's innate immune systems, protecting cells from infection by mobile genetic elements (MGEs). Their diversification has been recently associated with the emergence of particularly virulent lineages. However, we have previously found more R-M systems in genomes carrying more MGEs. Furthermore, it has been suggested that R-M systems might favor genetic transfer by producing recombinogenic double-stranded DNA ends. To test whether R-M systems favor or disfavor genetic exchanges, we analyzed their frequency with respect to the inferred events of homologous recombination and horizontal gene transfer within 79 bacterial species. Genetic exchanges were more frequent in bacteria with larger genomes and in those encoding more R-M systems. We created a recognition target motif predictor for Type II R-M systems that identifies genomes encoding systems with similar restriction sites. We found more genetic exchanges between these genomes, independently of their evolutionary distance. Our results reconcile previous studies by showing that R-M systems are more abundant in promiscuous species, wherein they establish preferential paths of genetic exchange within and between lineages with cognate R-M systems. Because the repertoire and/or specificity of R-M systems in bacterial lineages vary quickly, the preferential fluxes of genetic transfer within species are expected to constantly change, producing time-dependent networks of gene transfer.

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